The Complete Amomum kravanh Chloroplast Genome Sequence and Phylogenetic Analysis of the Commelinids.

Mingli Wu,Zhigang Hu,Shilin Chen,Xiwen Li,Qing Li

doi:10.3390/molecules22111875

Abstract

Amomum kravanh is an important edible and medicinal herb, the dried fruits of which are widely used in traditional herbal medicine as cardamom. We sequenced and analyzed the complete chloroplast (cp) genome of A. kravanh with herbgenomics technologies. The size of the A. kravanh cp genome was 162,766 bp, which consisted of long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,824 bp). The genome encoded 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. A total of 299 simple sequence repeats (SSRs) were identified in the A. kravanh cp genome, which provides an effective method to study species identification and population genetics of the medicinal plant. Moreover, one complement, 12 forward, 12 palindrome and two reverse repeats were detected. Comparative cp genome sequence analysis of four Zingiberaceae species indicated that their intergenic spacers are highly divergent, although the gene order, gene content and genome structure differed only minimally. In particular, there was a remarkable expansion of the IR regions in the A. kravanh cp genome. Phylogenetic analysis strongly supported a sister relationship between A. kravanh and Alpinia zerumbet. This study identified the unique characteristics of the A. kravanh cp genome and might provide valuable information for future studies aiming for Amomum identification, and provide insights into the taxonomy of the commelinids.

Highlights

As a major plant cell organelle, the chloroplast is crucial to the growth and development of plants through its roles in photosynthesis and secondary metabolic activities
The complete cp genome of A. kravanh was revealed as 162,766 bp in size, with a typical quadripartite structure (Table 1 and Figure 1)
The long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions were separated by a pair of inverted repeats (IRs; 29,824 bp each)

Summary

Introduction

As a major plant cell organelle, the chloroplast (cp) is crucial to the growth and development of plants through its roles in photosynthesis and secondary metabolic activities. Cp genomes have been widely used for species identification, investigation of phyletic evolution and genetic engineering because of their highly conserved nature and role in monolepsis. Development of sequencing technologies has led to a sharp increase in the number of cp genome sequences; much remains to be achieved, for medicinal species. No Amomum cp genome sequences have yet been reported, which has led to delays in investigation of the genetics and breeding of cardamom. Amomum kravanh (family Zingiberaceae) is one of the original types of cardamom plant, which is a significant traditional Chinese medicine that had been primarily imported from Thailand, Vietnam and Cambodia since the 1960s, and is widely cultivated in southern China.

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Conclusion